Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Poulsen, Jan Y ^a   Byrkjedal, Ingvar ^a   Willassen, Endre ^a   Rees, David ^a   Takeshima, Hirohiko ^b   Satoh, Takashi P ^c   Shinohara, Gento ^c   Nishida, Mutsumi ^b   Miya, Masaki ^d  

^a UNIVERSITY OF BERGEN   (Norway)

^b UNIVERSITY OF TOKYO   (Japan)

^c DEPARTMENT OF BOTANY   (Japan)

^d NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

Author keywords

Gene rearrangements; Mitogenomics; Myctophidae; Myctophiformes; Neoscopelidae; Non coding sequence; Phylogeny

Indexed keywords

ARRAY; BIOMASS; CLASSIFICATION; DIVERGENCE; GENE EXPRESSION; GENOMICS; MOLECULAR ANALYSIS; MORPHOLOGY; PHYLOGENETICS; PHYLOGENY; POPULATION DISTRIBUTION; RARE SPECIES; SPECIALIZATION; TAXONOMY; TELEOST;

LAMPANYCTINAE; MYCTOPHIDAE; MYCTOPHIFORMES; NEOSCOPELIDAE; NEOTELEOSTEI; NOTOLYCHNUS VALDIVIAE; PISCES; SOLIVOMER ARENIDENS;

TRANSFER RNA;

ANIMAL; ARTICLE; CLASSIFICATION; FISH; GENE ORDER; GENE REARRANGEMENT; GENETICS; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEA;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; FISHES; GENE ORDER; GENE REARRANGEMENT; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; RNA, TRANSFER;

EID: 84878358188     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-111     Document Type: Article

References (114)

1. Interrelationships of higher euteleostean fishes. Rosen DE, Interrelationships of Fishes London: Academic Press, Greenwood PH, Miles RS, Patterson C, 1973 397 513
2. Nelson JS, Fishes of the world Hoboken, New Jersey: John Wiley & Sons 2006
3. Osteology and relationships of the lanternfishes (family Myctophidae). Paxton JR, Bull Nat Hist Mus Los Angeles Cty 1972 13 1 81
4. A classification of the fishes of the family myctophidae. Fraser-Brunner A, Proc Zool Soc London 1949 118 1019 1106
5. Basal Ctenosquamate relationships and the interrelationships of the myctophiform (Scopelomorph) fishes. Stiassny MLJ, Interrelationships of Fishes San Diego: Academic, Stiassny MLJ, Parenti LR, Johnson GD, 1996 405 426
6. A review of the myctophid fishes of the pacific coast of the unites states and of lower California. Bolin RJ, Stanford Ichthyological Bull 1939 1 89 156
7. Myctophidae. Hulley AP, Encyclopedia of Fishes 2 San Diego: Academic, Paxton J, Eschmeyer WN, 1998 127 128
8. The olfactory epithelium of the lantern fish, Tarletonbeania crenularis (Myctophidae). Lawry JV, Z Zellforsch 1973 138 31 39 10.1007/BF00307076 4697125
9. Phylogeny of north American fireflies (coleoptera: lampyridae): implications for the evolution of light signals. Stanger-Hall KF, Lloyd JE, Hillis DM, Mol Phylogenet Evol 2007 45 33 49 10.1016/j.ympev.2007.05.013 17644427
10. Luminescent Properties of fishes from nearshore California Basins. Mensinger AF, Case FJ, J Exp Biol Ecol 1997 210 75 90 10.1016/S0022-0981(96) 02719-0
11. Bioluminescence in the ocean: origins of biological, chemical, and ecological diversity. Widder EA, Science 2010 328 704 708 10.1126/science. 1174269 20448176
12. Evidence of luminous bacterial symbionts in the light organs of myctophid and stomiiform fishes. Foran, J Evo Zool 1991 259 1 8
13. Bioluminescence of myctophid and stomiiform fishes is not due to bacterial luciferase. Haygood MG, Edwards DB, Mowlds G, Rosenblatt RH, J Exp Zool 1994 270 225 231 10.1002/jez.1402700212
14. Shimomura O, Bioluminescence. Chemical Principles and Methods World Scientific Publishing Singapore 2006
15. Bacterial origin of bioluminescence in marine animals. Leisman G, Cohn DH, Nealson KH, Science 1980 208 1271 1273 10.1126/science.208.4449.1271 17830813
16. Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes from unique lineages related to the genus Vibrio. Haygood MG, Distel DL, Nature 1993 363 154 156 10.1038/363154a0 7683390
17. Vision in lanternfish (myctophidae): adaptations for viewing bioluminescence in the deep-sea. Turner JR, White EM, Collins MA, Partridge JC, Douglas RH, Deep-sea Res 1 2009 56 1003 1017 10.1016/j.dsr.2009.01.007
18. The Visual pigments of a deep-sea myctophid fish Myctophum nitidulum Garman; an HPLC and spectroscopic description of a non-paired rhodopsin-porphyropsin system. Hasegawa EI, Sawada K, Abe K, Watanabe K, Uchikawa K, Okazaki Y, Toyama M, Douglas RH, J Fish Biol 2008 72 937 945 10.1111/j.1095-8649.2007.01772.x
19. The eyes of deeep-sea fish 1: Lens pigmentation, tapeta and visual pigments. Douglas RH, Partridge JC, Marshall NJ, Prog Retinal Eye Res 1998 17 597 636 10.1016/S1350-9462(98)00002-0
20. Diel vertical migration of myctophid fishes (family Myctophidae) in the transitional waters of the western North Pacific. Watanabe H, Moku M, Kawaguchi K, Ishimaru K, Ohno A, Fisheries Oceanography 1999 8 115 127 10.1046/j.1365-2419.1999.00103.x
21. Ceratoscopelus maderensis: peculiar sound-scattering layer identified with this myctophid fish. Backus RH, Craddock JE, Haedrich RL, Shores DL, Teal JM, Wing AS, Mead GW, Clarke WD, Science 1968 160 991 993 10.1126/science.160. 3831.991 5647856
22. Adaptive value of vertical migration: comments on the predation hypothesis and some alternatives. Kerfoot WC, Contrib Mar Sci 1985 27 91 113
23. Species abundance, sexual encounter and bioluminescent signaling in the deep sea. Herring PJ, Phil Trans Royal Soc London B 2000 355 1273 1276 10.1098/rstb.2000.0682
24. Phylogenetic analyses of myctophid fishes using morphological characters: Progress, problems, and future perspectives. Yamaguchi M, Japanese J Ichthyol 2000 47 87 107
25. A new genus and species of myctophid fish from the South-Central Pacific Ocean, with notes on related genera and the designation of a new tribe, Electronini. Wisner RL, Copeia 1963 1 24 28
26. The urodermals in lanternfish family myctophidae (Pisces: myctophiformes). Miyake T, Uyeno T, Copeia 1987 1 176 181
27. Development of lanternfishes (family myctophidae) in the California current. Part 1. Species with narrow-eyed larvae. Moser HG, Ahlstrom EH, Bull Nat Hist Mus Los Angeles Cty 1970 7 1 145
28. Development of the lanternfish, Scopelopsis multipunctatus Brauer 1906, with a discussion of its phylogenetic position in the family Myctophidae and its Role in a proposed mechanism for the evolution of photophore patterns in lanternfishes. Moser HG, Ahlstrom EH, Fish Bull 1972 70 541 564
29. Role of larval stages in systematic investigations of marine teleosts: a case study. Moser HG, Ahlstrom EH, Fish Bull 1974 72 391 413
30. Myctophidae: relationships. Paxton J, Ahlstrom EH, Moser HG, Ontogeny and Systematics of Fishes Special Publication 1, ASIH 1984 239 244
31. Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae). Yamaguchi M, Miya M, Okiyama M, Nishida M, Mol Phylogenet Evol 2000 15 103 114 10.1006/mpev.1999.0726 10764538
32. Speciation in the open ocean. Miya M, Nishida M, Nature 1997 389 803 804 10.1038/39774
33. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Miya M, Kawaguchi A, Nishida M, Mol Biol Evol 2001 18 1993 2009 10.1093/oxfordjournals.molbev.a003741 11606696
34. Sequence and organization of the human mitochondrial genome. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG, Nature 1981 290 457 465 10.1038/290457a0 7219534
35. Animal mitochondrial genomes. Boore JL, Nuc Acids Res 1999 27 1767 1780 10.1093/nar/27.8.1767
36. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Boore JL, Brown WM, Curr Opinion in Gen Dev 1998 8 668 674 10.1016/S0959-437X(98)80035-X
37. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Macey JR, Larson A, Ananjeva NB, Fang Z, Papenfuss TJ, Mol Biol Evol 1997 14 91 104 10.1093/oxfordjournals.molbev.a025706 9000757
38. Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. Moritz C, Brown WM, Proc Natl Acad Sci USA 1987 84 7183 7187 10.1073/pnas.84.20.7183 3478691
39. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. Boore JL, Computational Biology Series Volume 1 Dordrecht (The Netherlands): Kluwer Academic Publishing, Sankoff D, Nadeau J, 2000 133 147
40. Multiple independent origins of mitochondrial gene order in birds. Mindell DP, Sorenson MD, Dimcheff DE, Proc Nat Acad Sci 1998 95 10693 10697 10.1073/pnas.95.18.10693 9724766
41. Complete mtDNA Sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Lavrov DV, Boore JL, Brown WM, Mol Biol Evol 2002 19 163 169 10.1093/oxfordjournals.molbev. a004068 11801744
42. Personal webpage Jan Yde Poulsen http://jypichthyology.info
43. Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii" Ishiguro NB, Miya M, Nishida M, Mol Phylogenet Evol 2003 27 476 488 10.1016/S1055-7903(02)00418-9 12742752
44. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Miya M, Nishida M, Mol Phylogenet Evol 2000 17 437 455 10.1006/mpev.2000.0839 11133198
45. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Miya M, Nishida M, Mar Biotech 1999 1 416 426 10.1007/PL00011798
46. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M, Mol Phylogenet Evol 2003 26 121 138 10.1016/S1055-7903(02) 00332-9 12470944
47. Evolutionary history of anglerfishes (Teleostei:Lophiiformes): A mitogenomic perspective. Miya M, Pietsch TW, Orr JW, Arnold RJ, Satoh TP, Shedlock AM, Ho H-C, Shimazaki M, Yabe M, Nishida M, BMC Evol Biol 2010 10 58 10.1186/1471-2148-10-58 20178642
48. Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences. Satoh TP, Miya M, Endo H, Nishida M, Mol Phylogenet Evol 2006 40 129 138 10.1016/j.ympev.2006.02.014 16603389
49. Complete mitochondrial genome amplification. Cheng S, Higuchi R, Stoneking M, Nat Gen 1994 7 350 351 10.1038/ng0794-350
50. 4peaks version 1.7.2 http://www.mekentosj.com/science/4peaks
51. TextWrangler version 3.5.3 http://barebones.com/products/textwrangler
52. Maddison DR, Maddison WP, MacClade Version 4 Sunderland, Massachusetts: Sinauer Associates 2003
53. Sequencher version 4.10.1 http://genecodes.com
54. NCBI http://www.ncbi.nlm.nih.gov
55. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Lowe TM, Eddy SR, Nucleic Acids Res 1997 25 955 964 9023104
56. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Schattner P, Brooks AN, Lowe TM, Nucleic Acids Res 2005 33 686 689 10.1093/nar/gki366
57. A hidden Markov model for progressive multiple alignment. Löytynoja A, Milinkovitch MC, Bioinformatics 2003 19 1505 1513 10.1093/bioinformatics/ btg193 12912831
58. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Lanfear R, Calcott B, Ho SYW, Guindon S, Mol Biol Evol 2012 29 1695 1701 10.1093/molbev/mss020 22319168
59. Swofford DL, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 Sunderland, Massachusetts: Sinauer Associates 2003
60. Phylogenetic models of rate heterogeneity: a high performance computing perspective. Stamatakis A, Proc IPDPS 2006
61. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Stamatakis A, Bioinformatics 2006 22 2688 2690 10.1093/bioinformatics/btl446 16928733
62. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Yang Z, J Mol Evol 1994 39 306 314 10.1007/BF00160154 7932792
63. A new look at the statistical model identification. Akaike H, IEEE Trans Automatic Control 1974 19 716 723 10.1109/TAC.1974.1100705
64. Estimating the dimension of a model. Schwarz GE, Ann Stat 1978 6 461 464 10.1214/aos/1176344136
65. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO, BMC Evol Biol 2006 6 29 10.1186/1471-2148-6-29 16563161
66. Model of amino acid substitution in proteins encoded by mitochondrial DNA. Adachi J, Hasegawa M, J Mol Evol 1996 42 459 468 10.1007/BF02498640 8642615
67. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/ btg180 12912839
68. AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. Kumar S, Skjæveland Å Russell RJS, Enger P, Ruden T, Mevik BH, Burki F, Botnen A, Shalchian-Tabrizi K, BMC Bioinformatics 2009 10 357 10.1186/1471-2105-10-357 19863793
69. Rambaut A, Drummond AJ, Tracer version 1.5 http://tree.bio.ed.ac.uk/ software/tracer
70. Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Smith C, Heyne S, Richter AS, Will S, Backofen R, Nucleic Acids Res 2010 38 373 377 10.1093/nar/gkq316
71. RNAshapes: an integrated RNA analysis package based on abstract shapes. Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R, Bioinformatics 2006 22 500 503 10.1093/bioinformatics/btk010 16357029
72. VARNA: Interactive drawing and editing of the RNA secondary structure. Darty K, Denise A, Ponty Y, Bioinformatics 2009 25 1974 1975 10.1093/bioinformatics/btp250 19398448
73. An approximately unbiased test of phylogenetic tree selection. Shimodaira H, Syst Biol 2002 51 492 508 10.1080/10635150290069913 12079646
74. CONSEL: for assessing the confidence of phylogenetic tree selection. Shimodaira H, Hasegawa M, Bioinformatics 2001 17 1246 1247 10.1093/ bioinformatics/17.12.1246 11751242
75. Maddison WP, Maddison DR, Mesquite: a modular system for evolutionary analysis. Version 2.75 http://mesquiteproject.org
76. Structure of a ribonucleic acid. Holley RW, Apgar J, Everett GA, Madison JT, Marquisee M, Merrill SH, Penswick JR, Zamir A, Science 1965 147 1462 1465 10.1126/science.147.3664.1462 14263761
77. The Phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 mitochondrial genome sequences. Miya M, Satoh TP, Nishida M, Bio J Linn Soc 2005 85 289 306 10.1111/j.1095-8312.2005.00483.x
78. Resolution of ray-finned fish phylogeny and timing of diversification. Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL, PNAS 2012 109 13698 13703 10.1073/pnas.1206625109 22869754
79. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Lartillot N, Philippe H, Mol Biol Evol 2004 21 1095 1109 10.1093/molbev/msh112 15014145
80. Phylobayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Lartillot N, Lepage T, Blanquart S, Bioinformatics 2009 25 2286 2288 10.1093/bioinformatics/btp368 19535536
81. Two series of parapophyses in neoscopelid fishes (Teleostei: Myctophiformes). Miyashita T, Fujita K, Ichthyol Res 2000 47 143 148 10.1007/BF02684234
82. Otolith-morphology and its usage for higher systematical units, with special reference to the Myctophiformes s.l. Schwarzhans W, Meded Tert Kwart Geol 1978 15 167 185
83. An essay on euteleostean classification. Rosen DE, Am Mus Novit 1985 2827 1 45
84. A new genus and species of deep-sea fish of the family Myctophidae from the Philippine Islands. Miller RR, Proc US Nat Mus 1947 97 81 90 10.5479/si.00963801.97-3211.81
85. Interim account of family myctophidae. In fishes of the Western North Atlantic. Bolin RL, Mem Sears Foundation Mar Res 1 1966 5 190 191
86. Bioluminescence in fishes. Herring PJ, Morin JG, Bioluminescence in action London: Academic, Herring PJ, 1978 273 329
87. Mitochondrial intergenic spacer in fairy basslets (Serranidae: Anthiinae) and the simultaneous analysis of nucleotide and rearrangement data. Smith L, Smith KR, Wheeler WC, Am Mus Novit 2009 3652 1 10
88. Development and distribution of larvae and early juveniles of the commercial lanternfish, Lampanyctodes hectoris (günther), off the west coast of southern Africa with a discussion of phylogenetic relationships of the genus. Ahlstrom EH, Moser HG, O'Toole M, Bull Southern California Acad Sci 1976 75 138 152
89. Systematics and distribution of lanternfishes of the genera Lobianchia and Diaphus (Myctophidae) in the Indian Ocean. Nafpaktitis BG, Bull Nat His Mus Los Angeles County 1978 30 1 92
90. Taxonomy and distribution of the lanternfishes, genera Lobianchia and Diaphus, in the North Atlantic. Nafpaktitis BG, Dana-Report 1968 73 1 134
91. Taxonomy and distribution of the lanternfishes, genus Diaphus (Pisces, Myctophidae) in the Western Pacific, Eastern Indian Oceans and the Southeast Asian Seas. Kawaguchi K, Shimizu H, Bull Ocean Res Inst Univ Tokyo 1978 10 1 142
92. Iniomi. Myctophidae from the "Michael sars" north Atlantic deep-Sea expedition. Bolin RL, Rept Sci Res "Michael Sars" Deep-Sea Expd 1910 1959 4 1 45 10724406
93. Idiolychnus, a new genus of Myctophidae based on Diaphus urolampus. Nafpaktitis BG, Paxton JR, Copeia 1978 3 492 497
94. Parvilux, a new genus of myctophid fishes from the northeastern Pacific, with two new species. Hubbs CL, Wisner RL, Zool Mededelingen 1964 39 445 463
95. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL, Mol Phylogenet Evol 2004 33 22 31 10.1016/j.ympev.2004.05.003 15324836
96. Review of the lanternfish genus Lampadena with a description of a new species. Nafpaktitis BG, Paxton JR, Contributions Sci 1968 138 1 29
97. Nominal genera and species of lanternfishes (Family Myctophidae). Paxton JR, Contributions Sci Nat Hist Mus Los Angeles County 1979 322 1 28
98. Dorsadena yaquinae, a new species and genus of myctophid fish from the Eastern North Pacific Ocean. Coleman LR, Nafpaktitis BG, Contributions Sci 1972 225 1 11
99. A Review of the lanternfish genus Taaningichthys (family Myctophidae) with the description of a new species. Davy B, Fish Bull 1972 70 67 78
100. Preliminary investigations on the evolution of the tribe Electronini (Myctophiformes, Myctophidae). Hulley PA, Fishes of Antarctica: A Biological Overview Milano: Springer, Prisco GD, Pisano E, Clarke A, 1998 75 86
101. Myctophid fishes of the genus Myctophum in the Pacific and Indian Oceans. Kawaguchi K, Aioi K, J Oceanographical Soc Japan 1972 28 161 175 10.1007/BF02108760
102. New species of lanternfish of the genus Myctophum (Myctophidae, Pisces). Bekker VE, Borodulina OD, Voprosy Ikhtiologii 1971 11 418 426
103. Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae). Mabuchi K, Miya M, Satoh TP, Westneat MW, Nishida M, J Mol Evol 2004 59 287 297 10.1007/s00239-004-2621-z 15553084
104. Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae). Zhou Y, Zhang JY, Zheng RQ, Yu BG, Yang G, Gene 2009 447 86 96 10.1016/j.gene.2009.07.009 19631263
105. Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels. Inoue JG, Miya M, Tsukamoto K, Nishida M, Mol Biol Evol 2003 20 1917 1924 10.1093/molbev/msg206 12949142
106. A Hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Mauro DS, Gower DJ, Zardoya R, Wilkinson M, Mol Bio Evol 2006 23 227 234
107. Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates. Desjardins P, Morais R, J Mol Biol 1990 212 599 634 10.1016/0022-2836(90)90225-B 2329578
108. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Mueller RL, Boore JL, Mol Biol Evol 2005 22 2104 2112 10.1093/molbev/msi204 15987876
109. Sequence characterization of a unique intergenic spacer in Gadiformes mitochondrial DNA. Bakke IG, Shields F, Johansen S, Mar Biotech 1999 1 411 415 10.1007/PL00011797
110. Gene Rearrangements in snake mitochondrial genomes: Highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Kumazawa Y, Ota H, Nishida M, Ozawa T, Mol Biol Evol 1996 13 1242 1254 10.1093/oxfordjournals.molbev.a025690 8896377
111. Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar. Kurabayashi A, Sumida M, Yonekawa H, Glaw F, Vences M, Hasegawa M, Mol Biol Evol 2008 25 874 891 10.1093/molbev/msn031 18263605
112. Mitochondrial genome of the komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. Kumazawa Y, Endo H, DNA Res 2004 11 115 125 10.1093/dnares/11.2.115 15449544
113. Mitochondrial genomes of acrodont lizards: Timing of gene rearrangements and phylogenetic and biogeographic implications. Okajima Y, Kumazawa Y, BMC Evol Biol 2010 10 141 10.1186/1471-2148-10-141 20465814
114. Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: A new insight into gene order conservation. Satoh TP, Sato Y, Masuyama N, Miya M, Nishida M, BMC Genomics 2010 11 479 10.1186/1471-2164-11-479 20723209